United's hopes of a Premier League top-four finish took a heavy blow with last Sunday's defeat to Arsene Wenger's Gunners in north London - a match for which Mourinho left Marcus Rashford and Paul Pogba out of his starting line-up.
United, who hold a 1-0 lead from the first leg, will qualify for the Champions League if they win the Europa League, so Mourinho wasn't too concerned with the result against Arsenal.
Rooney has made just 22 United starts across all competitions and continuing questions over his viability at the top level have fuelled talk that his future lies away from Old Trafford.
"That's what he's waiting for".
United are fifth in the league, four points behind Manchester City with three games left, but while climbing above their rivals into fourth is probably beyond them they could still secure a spot in next season's Champions League by winning the Europa League.
"Do you think I enjoy the fact a big club like Arsenal is not winning trophies?"
"So you find yourself in the situation where he's going to have the last laugh at the end of the day".
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"I don't believe Celta dreams more than us, want to win more than us".
While United have struggled in the Premier League this term, the Portuguese could end his first season in the hotseat with a third trophy.
"Apart from that, I can not ask more from players who do not play one minute of football in the past seven weeks like Smalling and Mata".
He added: "I said a few weeks ago that we have to win every game and we didn't do that against Tottenham".
The youngster earned rave reviews from Jose Mourinho after the Arsenal game, with the manager telling Sky Sports: "I think he did an unbelievable job".
Here are some of the best pictures from Manchester United's latest training session. For me football is pretty much the same everywhere, the ball is round, but maybe tactically things are different than at other clubs I've played for. I'm really satisfied with my performance and the performance of the team, which is most important.
United have struggled to break into the Champions League qualification places all season, spending most of the campaign in fifth or sixth spot in the Premier League, and Sunday's loss leaves them in a hard position.
"So finally today they sing, they (swing) the scarves - it's nice for them".